diff picard_QualityScoreDistribution.xml @ 12:05087b27692a draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92

--- a/picard_QualityScoreDistribution.xml	Wed Nov 11 12:23:17 2015 -0500
+++ b/picard_QualityScoreDistribution.xml	Sun Nov 27 15:11:50 2016 -0500
@@ -4,21 +4,21 @@
     <import>picard_macros.xml</import>
   </macros>
   <expand macro="requirements">
-    <requirement type="package" version="3.1.2">R</requirement>
+    <requirement type="package" version="3.3.1">r</requirement>
   </expand>
-  <command>
+  <command detect_errors="exit_code"><![CDATA[
     @java_options@
     ##set up input files
 
     #set $reference_fasta_filename = "localref.fa"
     
     #if str( $reference_source.reference_source_selector ) == "history":
-        ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &amp;&amp;
+        ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &&
     #else:
         #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
     #end if
     
-    java -jar \$JAVA_JAR_PATH/picard.jar
+    picard
     QualityScoreDistribution
     INPUT="${inputFile}"
     OUTPUT="${outFile}"
@@ -34,7 +34,7 @@
     QUIET=true
     VERBOSITY=ERROR
   
-  </command>
+  ]]></command>
   <inputs>
     <param format="sam,bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
     <conditional name="reference_source">
@@ -80,9 +80,6 @@
     </test> 
   </tests>
   
-  <stdio>
-    <exit_code range="1:"  level="fatal"/>
-  </stdio>
   
   <help>